Downvoted comments whose font colors are adjusted to more closely match the background page color are still easy to read simply by highlighting them because the highlighted background color doesn't change, leaving you with outlined, legible characters. And it's actually quite tempting to read these comments since it takes such little effort to do so.
Adjusting the opacity property seems to affect both the font and the highlighted background, making it near impossible to read a comment set at, say, opacity 0.2. The only options you'd have to render the text legible would be either editing the css file, or copying/pasting the text elsewhere, both (I think) being too high-labor and making the effort just not worth it.
Edit: Tested a bit more, seems like opacity only seems to have a noticeable affect on legibility at around 0.4 and under. What about a combination of both systems whereby after hitting a certain threshold of negative karma, a greyed out comment is rendered more transparent? The idea is to make it difficult to read comments that are almost without a doubt inflammatory and uncivil. Often you'll see an endless stream of repetitive and replies made to a completely greyed out comment.
Perhaps I'll repeat a related point: if you notice a faded-out comment that's both substantive and civil, it's good community practice to give it a corrective upvote. This practice evolved on HN a long time ago, but we're asking people to do it more consciously now, because of our recent change to make some downvotes more powerful. When a comment has been downvoted unfairly, it usually only takes one or two corrective upvotes to get it back to par, so every user can make a big difference.